{"id":"https://openalex.org/W4401689426","doi":"https://doi.org/10.1186/s13326-024-00315-0","title":"Concretizing plan specifications as realizables within the OBO foundry","display_name":"Concretizing plan specifications as realizables within the OBO foundry","publication_year":2024,"publication_date":"2024-08-19","ids":{"openalex":"https://openalex.org/W4401689426","doi":"https://doi.org/10.1186/s13326-024-00315-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/39160586"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-024-00315-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-024-00315-0","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-024-00315-0","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-024-00315-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005828535","display_name":"William D. Duncan","orcid":"https://orcid.org/0000-0001-9625-1899"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William D. Duncan","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA. wdduncan@gmail.com","University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA. wdduncan@gmail.com","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030579890","display_name":"Matthew Diller","orcid":"https://orcid.org/0000-0001-6378-1703"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Diller","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006394765","display_name":"Damion Dooley","orcid":"https://orcid.org/0000-0002-8844-9165"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Damion Dooley","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC, CA, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC, CA, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076610873","display_name":"William R. Hogan","orcid":"https://orcid.org/0000-0002-9881-1017"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William R. Hogan","raw_affiliation_strings":["Medical College of Wisconsin, Milwaukee, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical College of Wisconsin, Milwaukee, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018629984","display_name":"John Beverley","orcid":"https://orcid.org/0000-0002-1118-1738"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John Beverley","raw_affiliation_strings":["University at Buffalo, Buffalo, NY, USA. johnbeve@buffalo.edu","University at Buffalo, Buffalo, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University at Buffalo, Buffalo, NY, USA. johnbeve@buffalo.edu","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"University at Buffalo, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5018629984"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.211,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.55767443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"15","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8708000183105469,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8708000183105469,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.10599999874830246,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0026000000070780516,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7003222703933716},{"id":"https://openalex.org/keywords/plan","display_name":"Plan (archaeology)","score":0.579146146774292},{"id":"https://openalex.org/keywords/foundry","display_name":"Foundry","score":0.49881672859191895},{"id":"https://openalex.org/keywords/engineering-management","display_name":"Engineering management","score":0.3970033824443817},{"id":"https://openalex.org/keywords/knowledge-management","display_name":"Knowledge management","score":0.37424159049987793},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3722333014011383},{"id":"https://openalex.org/keywords/manufacturing-engineering","display_name":"Manufacturing engineering","score":0.36119773983955383},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3536291718482971},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.3255748152732849},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.3201974034309387},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.174091637134552},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17136216163635254}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7003222703933716},{"id":"https://openalex.org/C2776505523","wikidata":"https://www.wikidata.org/wiki/Q4785468","display_name":"Plan (archaeology)","level":2,"score":0.579146146774292},{"id":"https://openalex.org/C2781087836","wikidata":"https://www.wikidata.org/wiki/Q13883136","display_name":"Foundry","level":2,"score":0.49881672859191895},{"id":"https://openalex.org/C110354214","wikidata":"https://www.wikidata.org/wiki/Q6314146","display_name":"Engineering management","level":1,"score":0.3970033824443817},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.37424159049987793},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3722333014011383},{"id":"https://openalex.org/C117671659","wikidata":"https://www.wikidata.org/wiki/Q11049265","display_name":"Manufacturing engineering","level":1,"score":0.36119773983955383},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3536291718482971},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3255748152732849},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.3201974034309387},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.174091637134552},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17136216163635254},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-024-00315-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-024-00315-0","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-024-00315-0","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:39160586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39160586","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11334599","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11334599","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11334599/pdf/13326_2024_Article_315.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:079a9d4a95d5462f95989956baae44bb","is_oa":true,"landing_page_url":"https://doaj.org/article/079a9d4a95d5462f95989956baae44bb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 15, Iss 1, Pp 1-14 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13326-024-00315-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-024-00315-0","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-024-00315-0","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4401689426.pdf","grobid_xml":"https://content.openalex.org/works/W4401689426.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1802346448","https://openalex.org/W2021074129","https://openalex.org/W3170771812","https://openalex.org/W4220666269","https://openalex.org/W6602130902"],"related_works":["https://openalex.org/W2782683786","https://openalex.org/W1989670675","https://openalex.org/W2347528996","https://openalex.org/W2362446285","https://openalex.org/W2117559011","https://openalex.org/W2359825503","https://openalex.org/W2390406441","https://openalex.org/W2030374199","https://openalex.org/W2366905977","https://openalex.org/W2352999985"],"abstract_inverted_index":{"BACKGROUND:":[0],"Within":[1],"the":[2,13,29,43,55,59,63,67,71,74,81,103,109,122,139,143,147,152,159,163,170,176,180,184,188,196,213,226,232,244,251,262,271,297],"Open":[3],"Biological":[4],"and":[5,62,142],"Biomedical":[6],"Ontology":[7],"(OBO)":[8],"Foundry,":[9],"many":[10],"ontologies":[11],"represent":[12],"execution":[14,148,178],"of":[15,73,108,151,198,246,253,264,276],"a":[16,20,24,32,46,51,222,236,248,258],"plan":[17,30,52,144,164,189,223,233,249,259,266],"specification":[18,53,224,234],"as":[19,235,293,295],"process":[21,64,229,245],"in":[22,80,127,162,187,195,301],"which":[23,40],"realizable":[25,60,68,123,140,153],"entity":[26,56,141,181,227],"that":[27,57,65,112,230,270],"concretizes":[28],"specification,":[31,165],"\"realizable":[33],"concretization\"":[34],"(RC),":[35],"is":[36,114,125,131,167,279,287],"realized.":[37],"This":[38],"representation,":[39],"we":[41,87],"call":[42],"\"RC-account\",":[44],"provides":[45],"straightforward":[47],"way":[48],"to":[49,54,98,156,173,179,220,225,256,289],"relate":[50,175],"bears":[58],"concretization":[61,124,154],"realizes":[66],"concretization.":[69],"However,":[70,284],"adequacy":[72],"RC-account":[75,104,110,171],"has":[76],"not":[77,101,115],"been":[78],"evaluated":[79],"scientific":[82],"literature.":[83],"In":[84],"this":[85,89,291,302],"manuscript,":[86],"provide":[88],"evaluation":[90],"and,":[91],"thereby,":[92],"give":[93],"ontology":[94],"developers":[95],"sound":[96],"reasons":[97],"use":[99,102,275],"or":[100,228],"pattern.":[105],"RESULTS:":[106],"Analysis":[107],"reveals":[111],"it":[113,130,166],"adequate":[116,280],"for":[117,206,281],"representing":[118,207],"failed":[119,177,208],"plans.":[120,200,209],"If":[121,146],"flawed":[126],"some":[128],"way,":[129],"unclear":[132,168],"what":[133],"(if":[134],"any)":[135],"relation":[136,219],"holds":[137],"between":[138],"specification.":[145,190],"(i.e.,":[149,274],"realization)":[150],"fails":[155],"carry":[157],"out":[158,183],"actions":[160],"given":[161,186],"under":[169],"how":[172],"directly":[174],"carrying":[182],"instructions":[185],"These":[191],"issues":[192],"are":[193],"exacerbated":[194],"presence":[197],"changing":[199],"CONCLUSIONS:":[201],"We":[202,268],"propose":[203],"two":[204],"solutions":[205,299],"The":[210,238],"first":[211,272],"uses":[212],"Common":[214],"Core":[215],"Ontologies":[216],"'prescribed":[217,277],"by'":[218],"connect":[221],"utilizes":[231],"guide.":[237],"second,":[239],"more":[240,285],"complex,":[241],"solution":[242,273],"incorporates":[243],"creating":[247],"(in":[250],"sense":[252],"an":[254],"intention":[255],"execute":[257],"specification)":[260],"into":[261],"representation":[263],"executing":[265],"specifications.":[267],"hypothesize":[269],"by')":[278],"most":[282],"situations.":[283],"research":[286],"needed":[288],"test":[290],"hypothesis":[292],"well":[294],"explore":[296],"other":[298],"presented":[300],"manuscript.":[303]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
